def exercise_asu():
sg_type = sgtbx.space_group_type("P 41")
asu = sgtbx.reciprocal_space_asu(sg_type)
miller_indices = flex.miller_index(((1, 2, 3), (3, 5, 0)))
for h in miller_indices:
h_eq = miller.sym_equiv_indices(sg_type.group(), h)
for i_eq in xrange(h_eq.multiplicity(False)):
h_i = h_eq(i_eq)
for anomalous_flag in (False, True):
a = miller.asym_index(sg_type.group(), asu, h_i.h())
assert a.h() == h
o = a.one_column(anomalous_flag)
assert o.i_column() == 0
t = a.two_column(anomalous_flag)
assert t.h() == h
assert (o.h() != h) == (t.i_column() == 1)
assert not anomalous_flag or (t.i_column() !=
0) == h_i.friedel_flag()
assert anomalous_flag or t.i_column() == 0
miller.map_to_asu(sg_type, False, miller_indices)
data = flex.double((0, 0))
miller.map_to_asu(sg_type, False, miller_indices, data)
miller.map_to_asu(sg_type, False, miller_indices, data, False)
miller.map_to_asu(sg_type, False, miller_indices, data, True)
data = flex.complex_double((0, 0))
miller.map_to_asu(sg_type, False, miller_indices, data)
data = flex.hendrickson_lattman(((1, 2, 3, 4), (2, 3, 4, 5)))
miller.map_to_asu(sg_type, False, miller_indices, data)
for sg_symbol in ("P 41", "P 31 1 2"):
exercise_map_to_asu(sg_symbol)
#
sg_type = sgtbx.space_group_type("P 2")
miller_indices = flex.miller_index(((1, 2, 3), (-1, -2, -3)))
assert not miller.is_unique_set_under_symmetry(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)
assert miller.is_unique_set_under_symmetry(space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)
assert list(
miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)) == [0]
assert list(
miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)) == [0, 1]
def exercise_asu():
sg_type = sgtbx.space_group_type("P 41")
asu = sgtbx.reciprocal_space_asu(sg_type)
miller_indices = flex.miller_index(((1,2,3), (3,5,0)))
for h in miller_indices:
h_eq = miller.sym_equiv_indices(sg_type.group(), h)
for i_eq in xrange(h_eq.multiplicity(False)):
h_i = h_eq(i_eq)
for anomalous_flag in (False,True):
a = miller.asym_index(sg_type.group(), asu, h_i.h())
assert a.h() == h
o = a.one_column(anomalous_flag)
assert o.i_column() == 0
t = a.two_column(anomalous_flag)
assert t.h() == h
assert (o.h() != h) == (t.i_column() == 1)
assert not anomalous_flag or (t.i_column() != 0) == h_i.friedel_flag()
assert anomalous_flag or t.i_column() == 0
miller.map_to_asu(sg_type, False, miller_indices)
data = flex.double((0,0))
miller.map_to_asu(sg_type, False, miller_indices, data)
miller.map_to_asu(sg_type, False, miller_indices, data, False)
miller.map_to_asu(sg_type, False, miller_indices, data, True)
data = flex.complex_double((0,0))
miller.map_to_asu(sg_type, False, miller_indices, data)
data = flex.hendrickson_lattman(((1,2,3,4),(2,3,4,5)))
miller.map_to_asu(sg_type, False, miller_indices, data)
for sg_symbol in ("P 41", "P 31 1 2"):
exercise_map_to_asu(sg_symbol)
#
sg_type = sgtbx.space_group_type("P 2")
miller_indices = flex.miller_index(((1,2,3), (-1,-2,-3)))
assert not miller.is_unique_set_under_symmetry(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)
assert miller.is_unique_set_under_symmetry(
space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)
assert list(miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)) == [0]
assert list(miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)) == [0,1]
def verify(sg_fcalc, sg_hl, sg_cns, p1_cns):
sg_phase_integrals = miller.array(
miller_set=miller.set(
crystal_symmetry=sg_fcalc,
indices=sg_cns.miller_indices,
anomalous_flag=sg_fcalc.anomalous_flag()),
data=sg_cns.hl).phase_integrals()
for h, cns_pi, miller_pi in zip(sg_cns.miller_indices,
sg_cns.pi.data,
sg_phase_integrals.data()):
if (abs(cns_pi - miller_pi) > 1.e-2):
print "Error:", h, cns_pi, miller_pi
if (0): return
raise AssertionError
#
p1_phase_integrals = miller.array(
miller_set=miller.set(
crystal_symmetry=sg_fcalc.cell_equivalent_p1(),
indices=p1_cns.miller_indices,
anomalous_flag=sg_fcalc.anomalous_flag()),
data=p1_cns.hl).phase_integrals()
for h, cns_pi, miller_pi in zip(p1_cns.miller_indices,
p1_cns.pi.data,
p1_phase_integrals.data()):
if (abs(cns_pi - miller_pi) > 1.e-2):
print "Error:", h, cns_pi, miller_pi
if (0): return
raise AssertionError
#
space_group = sg_fcalc.space_group()
asu = sg_fcalc.space_group_info().reciprocal_space_asu()
lookup_dict = miller.make_lookup_dict(sg_fcalc.indices())
for p1_i, h in enumerate(p1_cns.miller_indices):
h_asu = miller.asym_index(space_group, asu, h)
h_eq = h_asu.one_column(sg_fcalc.anomalous_flag())
fcalc_asu = h_eq.complex_eq(p1_cns.fcalc.data[p1_i])
hl_asu = h_eq.hendrickson_lattman_eq(p1_cns.hl[p1_i])
sg_i = lookup_dict[h_eq.h()]
assert abs(sg_fcalc.data()[sg_i] - fcalc_asu) < 1.e-2
if (not approx_equal(sg_hl[sg_i], hl_asu, eps=1.e-2)):
print "Error:", sg_fcalc.space_group_info()
print sg_fcalc.indices()[sg_i]
print "i:", sg_hl[sg_i]
print "o:", hl_asu
if (0): return
raise AssertionError
def verify(sg_fcalc, sg_hl, sg_cns, p1_cns):
sg_phase_integrals = miller.array(miller_set=miller.set(
crystal_symmetry=sg_fcalc,
indices=sg_cns.miller_indices,
anomalous_flag=sg_fcalc.anomalous_flag()),
data=sg_cns.hl).phase_integrals()
for h, cns_pi, miller_pi in zip(sg_cns.miller_indices, sg_cns.pi.data,
sg_phase_integrals.data()):
if (abs(cns_pi - miller_pi) > 1.e-2):
print("Error:", h, cns_pi, miller_pi)
if (0): return
raise AssertionError
#
p1_phase_integrals = miller.array(miller_set=miller.set(
crystal_symmetry=sg_fcalc.cell_equivalent_p1(),
indices=p1_cns.miller_indices,
anomalous_flag=sg_fcalc.anomalous_flag()),
data=p1_cns.hl).phase_integrals()
for h, cns_pi, miller_pi in zip(p1_cns.miller_indices, p1_cns.pi.data,
p1_phase_integrals.data()):
if (abs(cns_pi - miller_pi) > 1.e-2):
print("Error:", h, cns_pi, miller_pi)
if (0): return
raise AssertionError
#
space_group = sg_fcalc.space_group()
asu = sg_fcalc.space_group_info().reciprocal_space_asu()
lookup_dict = miller.make_lookup_dict(sg_fcalc.indices())
for p1_i, h in enumerate(p1_cns.miller_indices):
h_asu = miller.asym_index(space_group, asu, h)
h_eq = h_asu.one_column(sg_fcalc.anomalous_flag())
fcalc_asu = h_eq.complex_eq(p1_cns.fcalc.data[p1_i])
hl_asu = h_eq.hendrickson_lattman_eq(p1_cns.hl[p1_i])
sg_i = lookup_dict[h_eq.h()]
assert abs(sg_fcalc.data()[sg_i] - fcalc_asu) < 1.e-2
if (not approx_equal(sg_hl[sg_i], hl_asu, eps=1.e-2)):
print("Error:", sg_fcalc.space_group_info())
print(sg_fcalc.indices()[sg_i])
print("i:", sg_hl[sg_i])
print("o:", hl_asu)
if (0): return
raise AssertionError
